SUPERFAMILY 1.75 HMM library and genome assignments server


Virus attachment protein globular domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Virus attachment protein globular domain [ 49834]
Superfamily:   Virus attachment protein globular domain [ 49835] (3)
Families:   Adenovirus fiber protein "knob" domain [ 49836]
  Reovirus attachment protein sigma 1 head domain [ 69225]
  Lactophage receptor-binding protein head domain [ 141122] (2)


Superfamily statistics
Genomes (8) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 8 0 14
Proteins 8 0 14


Functional annotation
General category Other
Detailed category Viral proteins

Document:
Function annotation of SCOP domain superfamilies

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processHost-virus interaction0Moderately InformativeDirect
Biological processVirus entry into host cell0InformativeDirect
Cellular componentCapsid protein0InformativeDirect
Cellular componentHost nucleus0InformativeDirect
Developmental stageLate protein0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008982 SSF49835 Protein matches
Abstract

The viral attachment protein domain forms part of the fibre proteins in adenoviruses [PubMed10567268], and the sigma 1 protein in reoviruses [PubMed11782420]. Both proteins are trimers that contain fibrous tails and globular heads (reovirus), or knobs (adenovirus), which are structurally very similar. Both domain cores consist of eight anti-parallel beta-sheets, forming either a beta sandwich (fibre knob), or a beta-barrel (sigma 1 head), with a long loop containing an alpha helix. The remaining loops tend to be longer in the fibre knob. Functionally both the fibre knob and the sigma 1 head are involved in binding selectively to cell surface receptors. The reoviruses bind JAM (junction adhesion molecule), while the adenoviruses use the CAR (Coxsackievirus and adenovirus) receptor, with the exception of subgroup B adenoviruses [PubMed11437664].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

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Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 10 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Virus attachment protein globular domain domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 10 hidden Markov models representing the Virus attachment protein globular domain superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · UniProtKB KeyWords (KW) · Internal database links ]